rs2468168

Variant names:

• chr8-119157399-T-C
• rs2468168
• XR_928585.3:n.86+5320T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_928585.3(LOC105375725):​n.86+5320T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,100 control chromosomes in the GnomAD database, including 40,001 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.72 (40001 hom., cov: 32)
• Consequence: LOC105375725 XR_928585.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.12
• Publications: 2 publications found

Genes affected

LOC105375725 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108932 AN: 151982 Hom.: 39949 Cov.: 32

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.736

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.717 AC: 109037 AN: 152100 Hom.: 40001 Cov.: 32 AF XY: 0.713 AC XY: 53035 AN XY: 74348

African (AFR) AF: 0.875 AC: 36334 AN: 41544

American (AMR) AF: 0.632 AC: 9654 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2544 AN: 3470

East Asian (EAS) AF: 0.689 AC: 3558 AN: 5162

South Asian (SAS) AF: 0.591 AC: 2848 AN: 4820

European-Finnish (FIN) AF: 0.641 AC: 6774 AN: 10576

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.662 AC: 44999 AN: 67948

Other (OTH) AF: 0.740 AC: 1563 AN: 2112

Alfa AF: 0.626 Hom.: 2220

Bravo AF: 0.722

Asia WGS AF: 0.706 AC: 2461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0040
DANN	Benign	0.26
PhyloP100		-5.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2468168; hg19: chr8-120169638;